Haplanthodes (Acanthaceae) is an Indian endemic genus with four species. It is closely related to Andrographis which is also mainly distributed in India. Haplanthodes differs from Andrographis by the presence of cladodes in the inflorescences, subactinomorphic flowers, stamens included within the corolla tube, pouched stamens and oblate pollen grains. To understand the phylogenetic relationship of Haplanthodes, Andrographis and Haplanthus, which are putatively closely related taxa, we used four plastid markers, matK, rbcL, psbA-trnH and trnGR to construct a molecular phylogeny. Our results established the monophyly of Haplanthodes and revealed a sister relationship to Andrographis and Haplanthus. Further, to understand the historical biogeography of the genus, we inferred the divergence time and performed an ancestral area reconstruction. Our analyses suggest that Haplanthodes evolved during Late Miocene 5.85 Ma (95%HPD: 2.18–10.34 Ma) in peninsular India where it might have shared a common ancestor with Andrographis. To understand character evolution, the ancestral states of important morphological characters were inferred and discussed based on the equal rate model. The generic status of Haplanthus was not resolved due to incomplete sampling.